tbuckley/cabot-search huggingface dataset:
Plk1 Inhibitors and Abiraterone Synergistically Disrupt Mitosis and Kill Cancer Cells of Disparate Origin Independently of Androgen Receptor Signaling
Authors: Jesse C. Patterson, Andreas Varkaris, Peter J.P. Croucher, Maya Ridinger, Susan Dalrymple, Mannan Nouri, Fang Xie, Shohreh Varmeh, Oliver Jonas, Matthew A. Whitman, Sen Chen, Saleh Rashed, Lovemore Makusha, Jun Luo, John T. Isaacs, Mark G. Erlander, David J. Einstein, Steven P. Balk, Michael B. Yaffe
Journal: Cancer Research (2022)

Abstract Abiraterone is a standard treatment for metastatic castrate-resistant prostate cancer (mCRPC) that slows disease progression by abrogating androgen synthesis and antagonizing the androgen receptor (AR). Here we report that inhibitors of the mitotic regulator polo-like kinase-1 (Plk1), including the clinically active third-generation Plk1 inhibitor onvansertib, synergizes with abiraterone in vitro and in vivo to kill a subset of cancer cells from a wide variety of tumor types in an androgen-independent manner. Gene-expression analysis identified an AR-independent synergy-specific gene set signature upregulated upon abiraterone treatment that is dominated by pathways related to mitosis and the mitotic spindle. Abiraterone treatment alone caused defects in mitotic spindle orientation, failure of complete chromosome condensation, and improper cell division independently of its effects on AR signaling. These effects, although mild following abiraterone monotherapy, resulted in profound sensitization to the antimitotic effects of Plk1 inhibition, leading to spindle assembly checkpoint-dependent mitotic cancer cell death and entosis. In a murine patient-derived xenograft model of abiraterone-resistant metastatic castration-resistant prostate cancer (mCRPC), combined onvansertib and abiraterone resulted in enhanced mitotic arrest and dramatic inhibition of tumor cell growth compared with either agent alone. Overall, this work establishes a mechanistic basis for the phase II clinical trial (NCT03414034) testing combined onvansertib and abiraterone in mCRPC patients and indicates this combination may have broad utility for cancer treatment. Significance: Abiraterone treatment induces mitotic defects that sensitize cancer cells to Plk1 inhibition, revealing an AR-independent mechanism for this synergistic combination that is applicable to a variety of cancer types.
T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy
Authors: Meredith L. Frank, Kaylene Lu, Can Erdogan, Yi Han, Jian Hu, Tao Wang, John V. Heymach, Jianjun Zhang, Alexandre Reuben
Journal: Clinical Cancer Research (2022)

Abstract T cells are integral components of the adaptive immune system, and their responses are mediated by unique T-cell receptors (TCR) that recognize specific antigens from a variety of biological contexts. As a result, analyzing the T-cell repertoire offers a better understanding of immune responses and of diseases like cancer. Next-generation sequencing technologies have greatly enabled the high-throughput analysis of the TCR repertoire. On the basis of our extensive experience in the field from the past decade, we provide an overview of TCR sequencing, from the initial library preparation steps to sequencing and analysis methods and finally to functional validation techniques. With regards to data analysis, we detail important TCR repertoire metrics and present several computational tools for predicting antigen specificity. Finally, we highlight important applications of TCR sequencing and repertoire analysis to understanding tumor biology and developing cancer immunotherapies.
Anti-BCMA/CD19 CAR T Cells with Early Immunomodulatory Maintenance for Multiple Myeloma Responding to Initial or Later-Line Therapy
Authors: Alfred L. Garfall, Adam D. Cohen, Sandra P. Susanibar-Adaniya, Wei-Ting Hwang, Dan T. Vogl, Adam J. Waxman, Simon F. Lacey, Vanessa E. Gonzalez, Joseph A. Fraietta, Minnal Gupta, Irina Kulikovskaya, Lifeng Tian, Fang Chen, Natalka Koterba, Robert L. Bartoszek, Margaret Patchin, Rong Xu, Gabriela Plesa, Don L. Siegel, Andrea Brennan, Anne Marie Nelson, Regina Ferthio, Angela Cosey, Kim-Marie Shea, Rachel Leskowitz, Megan Four, Wesley V. Wilson, Fei Miao, Eric Lancaster, Beatriz M. Carreno, Gerald P. Linette, Elizabeth O. Hexner, Regina M. Young, Dexiu Bu, Keith G. Mansfield, Jennifer L. Brogdon, Carl H. June, Michael C. Milone, Edward A. Stadtmauer
Journal: Blood Cancer Discovery (2022)

Abstract We conducted a phase I clinical trial of anti-BCMA chimeric antigen receptor T cells (CART-BCMA) with or without anti-CD19 CAR T cells (huCART19) in multiple myeloma (MM) patients responding to third- or later-line therapy (phase A, N = 10) or high-risk patients responding to first-line therapy (phase B, N = 20), followed by early lenalidomide or pomalidomide maintenance. We observed no high-grade cytokine release syndrome (CRS) and only one instance of low-grade neurologic toxicity. Among 15 subjects with measurable disease, 10 exhibited partial response (PR) or better; among 26 subjects responding to prior therapy, 9 improved their response category and 4 converted to minimal residual disease (MRD)–negative complete response/stringent complete response. Early maintenance therapy was safe, feasible, and coincided in some patients with CAR T-cell reexpansion and late-onset, durable clinical response. Outcomes with CART-BCMA + huCART19 were similar to CART-BCMA alone. Collectively, our results demonstrate favorable safety, pharmacokinetics, and antimyeloma activity of dual-target CAR T-cell therapy in early lines of MM treatment. Significance: CAR T cells in early lines of MM therapy could be safer and more effective than in the advanced setting, where prior studies have focused. We evaluated the safety, pharmacokinetics, and efficacy of CAR T cells in patients with low disease burden, responding to current therapy, combined with standard maintenance therapy. This article is highlighted in the In This Issue feature, p. 101
Oncogenic KRAS signaling drives evasion of innate immune surveillance in lung adenocarcinoma by activating CD47
Authors: Huanhuan Hu, Rongjie Cheng, Yanbo Wang, Xiaojun Wang, Jianzhuang Wu, Yan Kong, Shoubin Zhan, Zhen Zhou, Hongyu Zhu, Ranran Yu, Gaoli Liang, Qingyan Wang, Xiaoju Zhu, Chen-Yu Zhang, Rong Yin, Chao Yan, Xi Chen
Journal: Journal of Clinical Investigation (2022)

KRAS is one of the most frequently activated oncogenes in human cancers. Although the role of KRAS mutation in tumorigenesis and tumor maintenance has been extensively studied, the relationship between KRAS and the tumor immune microenvironment is not fully understood. Here, we identified a role of KRAS in driving tumor evasion from innate immune surveillance. In samples of lung adenocarcinoma from patients and Kras-driven genetic mouse models of lung cancer, mutant KRAS activated the expression of cluster of differentiation 47 (CD47), an antiphagocytic signal in cancer cells, leading to decreased phagocytosis of cancer cells by macrophages. Mechanistically, mutant KRAS activated PI3K/STAT3 signaling, which restrained miR-34a expression and relieved the posttranscriptional repression of miR-34a on CD47. In 3 independent cohorts of patients with lung cancer, the KRAS mutation status positively correlated with CD47 expression. Therapeutically, disruption of the KRAS/CD47 signaling axis with KRAS siRNA, the KRASG12C inhibitor AMG 510, or a miR-34a mimic suppressed CD47 expression, enhanced the phagocytic capacity of macrophages, and restored innate immune surveillance. Our results reveal a direct mechanistic link between active KRAS and innate immune evasion and identify CD47 as a major effector underlying the KRAS-mediated immunosuppressive tumor microenvironment.
Aflibercept more effectively weans patients with neovascular age-related macular degeneration off therapy compared with bevacizumab
Authors: Xuan Cao, Jaron Castillo Sanchez, Tapan P. Patel, Zhiyong Yang, Chuanyu Guo, Danyal Malik, Anuoluwapo Sopeyin, Silvia Montaner, Akrit Sodhi
Journal: Journal of Clinical Investigation (2022)

BACKGROUNDStudies assessing the efficacy of therapies for neovascular age-related macular degeneration (nvAMD) have demonstrated that aflibercept may have a longer treatment interval than its less-expensive alternative, bevacizumab. However, whether this benefit justifies the additional cost of aflibercept remains under debate. We have recently reported that a treat-and-extend-pause/monitor approach can be used to successfully wean 31% of patients with nvAMD off anti-VEGF therapy. Here, we examined whether the choice of therapy influences the outcomes of this approach.METHODSIn this retrospective analysis, 122 eyes of 106 patients with nvAMD underwent 3 consecutive monthly injections with either aflibercept (n = 70) or bevacizumab (n = 52), followed by a treat-and-extend protocol, in which the decision to extend the interval between treatments was based on visual acuity, clinical exam, and the presence or absence of fluid on optical coherence tomography. Eyes that remained stable 12 weeks from their prior treatment were given a 6-week trial of holding further treatment, followed by quarterly monitoring. Treatment was resumed for worsening vision, clinical exam, or optical coherence tomography findings.RESULTSAt the end of 1 year, eyes receiving bevacizumab had similar vision but required more injections (8.7 ± 0.3 treatments vs. 7.2 ± 0.3 treatments) compared with eyes receiving aflibercept. However, eyes treated with aflibercept were almost 3 times more likely to be weaned off treatment (43% vs. 15%) compared with eyes treated with bevacizumab at the end of 1 year.CONCLUSIONThese observations expose an advantage of aflibercept over bevacizumab and have important clinical implications for the selection of therapy for patients with nvAMD.FUNDINGThis work was supported by the National Eye Institute, NIH grants R01EY029750 and R01EY025705, Research to Prevent Blindness, the Alcon Young Investigator Award from the Alcon Research Institute, and the Branna and Irving Sisenwein Professorship in Ophthalmology.
A phase I/II study on intracerebroventricular tralesinidase alfa in patients with Sanfilippo syndrome type B
Authors: Nicole Muschol, Anja Koehn, Katharina von Cossel, Ilyas Okur, Fatih Ezgu, Paul Harmatz, Maria J. de Castro Lopez, Maria Luz Couce, Shuan-Pei Lin, Spyros Batzios, Maureen Cleary, Martha Solano, Igor Nestrasil, Brian Kaufman, Adam J. Shaywitz, Stephen M. Maricich, Bernice Kuca, Joseph Kovalchin, Eric Zanelli
Journal: Journal of Clinical Investigation (2022)

BackgroundSanfilippo type B is a mucopolysaccharidosis (MPS) with a major neuronopathic component characterized by heparan sulfate (HS) accumulation due to mutations in the NAGLU gene encoding alfa-N-acetyl-glucosaminidase. Enzyme replacement therapy for neuronopathic MPS requires efficient enzyme delivery throughout the brain in order to normalize HS levels, prevent brain atrophy, and potentially delay cognitive decline.MethodsIn this phase I/II open-label study, patients with MPS type IIIB (n = 22) were treated with tralesinidase alfa administered i.c.v. The patients were monitored for drug exposure; total HS and HS nonreducing end (HS-NRE) levels in both cerebrospinal fluid (CSF) and plasma; anti-drug antibody response; brain, spleen, and liver volumes as measured by MRI; and cognitive development as measured by age-equivalent (AEq) scores.ResultsIn the Part 1 dose escalation (30, 100, and 300 mg) phase, a 300 mg dose of tralesinidase alfa was necessary to achieve normalization of HS and HS-NRE levels in the CSF and plasma. In Part 2, 300 mg tralesinidase alfa sustained HS and HS-NRE normalization in the CSF and stabilized cortical gray matter volume (CGMV) over 48 weeks of treatment. Resolution of hepatomegaly and a reduction in spleen volume were observed in most patients. Significant correlations were also established between the change in cognitive AEq score and plasma drug exposure, plasma HS-NRE levels, and CGMV.ConclusionAdministration of tralesinidase alfa i.c.v. effectively normalized HS and HS-NRE levels as a prerequisite for clinical efficacy. Peripheral drug exposure data suggest a role for the glymphatic system in altering tralesinidase alfa efficacy.Trial registrationClinicaltrials.gov NCT02754076.FUNDINGBioMarin Pharmaceutical Inc. and Allievex Corporation.
Taxonomy of fibroblasts and progenitors in the synovial joint at single-cell resolution
Authors: Fraser L Collins, Anke J Roelofs, Rebecca A Symons, Karolina Kania, Ewan Campbell, Elaina S R Collie-duguid, Anna H K Riemen, Susan M Clark, Cosimo De Bari
Journal: Annals of the Rheumatic Diseases (2022)

Objectives Fibroblasts in synovium include fibroblast-like synoviocytes (FLS) in the lining and Thy1 + connective-tissue fibroblasts in the sublining. We aimed to investigate their developmental origin and relationship with adult progenitors. Methods To discriminate between Gdf5 -lineage cells deriving from the embryonic joint interzone and other Pdgfrα -expressing fibroblasts and progenitors, adult Gdf5-Cre;Tom;Pdgfrα-H2BGFP mice were used and cartilage injury was induced to activate progenitors. Cells were isolated from knees, fibroblasts and progenitors were sorted by fluorescence-activated cell-sorting based on developmental origin, and analysed by single-cell RNA-sequencing. Flow cytometry and immunohistochemistry were used for validation. Clonal-lineage mapping was performed using Gdf5-Cre;Confetti mice. Results In steady state, Thy1 + sublining fibroblasts were of mixed ontogeny. In contrast, Thy1-Prg4 + lining fibroblasts predominantly derived from the embryonic joint interzone and included Prg4 -expressing progenitors distinct from molecularly defined FLS. Clonal-lineage tracing revealed compartmentalisation of Gdf5 -lineage fibroblasts between lining and sublining. Following injury, lining hyperplasia resulted from proliferation and differentiation of Prg4 -expressing progenitors, with additional recruitment of non- Gdf5 -lineage cells, into FLS. Consistent with this, a second population of proliferating cells, enriched near blood vessels in the sublining, supplied activated multipotent cells predicted to give rise to Thy1 + fibroblasts, and to feed into the FLS differentiation trajectory. Transcriptional programmes regulating fibroblast differentiation trajectories were uncovered, identifying Sox5 and Foxo1 as key FLS transcription factors in mice and humans. Conclusions Our findings blueprint a cell atlas of mouse synovial fibroblasts and progenitors in healthy and injured knees, and provide novel insights into the cellular and molecular principles governing the organisation and maintenance of adult synovial joints.
Longitudinal analysis of serum neutralization of SARS-CoV-2 Omicron BA.2, BA.4, and BA.5 in patients receiving monoclonal antibodies
Authors: Timothée Bruel, Karl Stéfic, Yann Nguyen, Donatella Toniutti, Isabelle Staropoli, Françoise Porrot, Florence Guivel-Benhassine, William-Henry Bolland, Delphine Planas, Jérôme Hadjadj, Lynda Handala, Cyril Planchais, Matthieu Prot, Etienne Simon-Lorière, Emmanuel André, Guy Baele, Lize Cuypers, Luc Mouthon, Hugo Mouquet, Julian Buchrieser, Aymeric Sève, Thierry Prazuck, Piet Maes, Benjamin Terrier, Laurent Hocqueloux, Olivier Schwartz
Journal: Cell Reports Medicine (2022)

The emergence of Omicron sublineages impacts the therapeutic efficacy of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monoclonal antibodies (mAbs). Here, we evaluate neutralization and antibody-dependent cellular cytotoxicity (ADCC) activities of 6 therapeutic mAbs against Delta, BA.2, BA.4, and BA.5. The Omicron subvariants escape most antibodies but remain sensitive to bebtelovimab and cilgavimab. Consistent with their shared spike sequence, BA.4 and BA.5 display identical neutralization profiles. Sotrovimab is the most efficient at eliciting ADCC. We also analyze 121 sera from 40 immunocompromised individuals up to 6 months after infusion of Ronapreve (imdevimab + casirivimab) or Evusheld (cilgavimab + tixagevimab). Sera from Ronapreve-treated individuals do not neutralize Omicron subvariants. Evusheld-treated individuals neutralize BA.2 and BA.5, but titers are reduced. A longitudinal evaluation of sera from Evusheld-treated patients reveals a slow decay of mAb levels and neutralization, which is faster against BA.5. Our data shed light on antiviral activities of therapeutic mAbs and the duration of effectiveness of Evusheld pre-exposure prophylaxis.
Human early syncytiotrophoblasts are highly susceptible to SARS-CoV-2 infection
Authors: Degong Ruan, Zi-Wei Ye, Shuofeng Yuan, Zhuoxuan Li, Weiyu Zhang, Chon Phin Ong, Kaiming Tang, Timothy Theodore Ka Ki Tam, Jilong Guo, Yiyi Xuan, Yunying Huang, Qingqing Zhang, Cheuk-Lun Lee, Liming Lu, Philip C.N. Chiu, William S.B. Yeung, Fang Liu, Dong-Yan Jin, Pentao Liu
Journal: Cell Reports Medicine (2022)

Direct in vivo investigation of human placenta trophoblast's susceptibility to SARS-CoV-2 is challenging. Here we report that human trophoblast stem cells (hTSCs) and their derivatives are susceptible to SARS-CoV-2 infection, which reveals heterogeneity in hTSC cultures. Early syncytiotrophoblasts (eSTBs) generated from hTSCs have enriched transcriptomic features of peri-implantation trophoblasts, express high levels of angiotensin-converting enzyme 2 (ACE2), and are productively infected by SARS-CoV-2 and its Delta and Omicron variants to produce virions. Antiviral drugs suppress SARS-CoV-2 replication in eSTBs and antagonize the virus-induced blockage of STB maturation. Although less susceptible to SARS-CoV-2 infection, trophoblast organoids originating from hTSCs show detectable viral replication reminiscent of the uncommon placental infection. These findings implicate possible risk of COVID-19 infection in peri-implantation embryos, which may go unnoticed. Stem cell-derived human trophoblasts such as eSTBs can potentially provide unlimited amounts of normal and genome-edited cells and facilitate coronavirus research and antiviral discovery.
On the usability of synthetic data for improving the robustness of deep learning-based segmentation of cardiac magnetic resonance images
Authors: Yasmina Al Khalil, Sina Amirrajab, Cristian Lorenz, Jürgen Weese, Josien Pluim, Marcel Breeuwer
Journal: Medical Image Analysis (2022)

Deep learning-based segmentation methods provide an effective and automated way for assessing the structure and function of the heart in cardiac magnetic resonance (CMR) images. However, despite their state-of-the-art performance on images acquired from the same source (same scanner or scanner vendor) as images used during training, their performance degrades significantly on images coming from different domains. A straightforward approach to tackle this issue consists of acquiring large quantities of multi-site and multi-vendor data, which is practically infeasible. Generative adversarial networks (GANs) for image synthesis present a promising solution for tackling data limitations in medical imaging and addressing the generalization capability of segmentation models. In this work, we explore the usability of synthesized short-axis CMR images generated using a segmentation-informed conditional GAN, to improve the robustness of heart cavity segmentation models in a variety of different settings. The GAN is trained on paired real images and corresponding segmentation maps belonging to both the heart and the surrounding tissue, reinforcing the synthesis of semantically-consistent and realistic images. First, we evaluate the segmentation performance of a model trained solely with synthetic data and show that it only slightly underperforms compared to the baseline trained with real data. By further combining real with synthetic data during training, we observe a substantial improvement in segmentation performance (up to 4% and 40% in terms of Dice score and Hausdorff distance) across multiple data-sets collected from various sites and scanner. This is additionally demonstrated across state-of-the-art 2D and 3D segmentation networks, whereby the obtained results demonstrate the potential of the proposed method in tackling the presence of the domain shift in medical data. Finally, we thoroughly analyze the quality of synthetic data and its ability to replace real MR images during training, as well as provide an insight into important aspects of utilizing synthetic images for segmentation.
Functional proteomic profiling links deficient DNA clearance with increased mortality in individuals with severe COVID-19 pneumonia
Authors: Iker Valle Aramburu, Dennis Hoving, Spyros I. Vernardis, Martha C.F. Tin, Marianna Ioannou, Mia I. Temkin, Nathalia M. De Vasconcelos, Vadim Demichev, Elisa Theresa Helbig, Lena Lippert, Klaus Stahl, Matthew White, Helena Radbruch, Jana Ihlow, David Horst, Scott T. Chiesa, John E. Deanfield, Sascha David, Christian Bode, Florian Kurth, Markus Ralser, Venizelos Papayannopoulos
Journal: Immunity (2022)

The factors that influence survival during severe infection are unclear. Extracellular chromatin drives pathology, but the mechanisms enabling its accumulation remain elusive. Here, we show that in murine sepsis models, splenocyte death interferes with chromatin clearance through the release of the DNase I inhibitor actin. Actin-mediated inhibition was compensated by upregulation of DNase I or the actin scavenger gelsolin. Splenocyte death and neutrophil extracellular trap (NET) clearance deficiencies were prevalent in individuals with severe COVID-19 pneumonia or microbial sepsis. Activity tracing by plasma proteomic profiling uncovered an association between low NET clearance and increased COVID-19 pathology and mortality. Low NET clearance activity with comparable proteome associations was prevalent in healthy donors with low-grade inflammation, implicating defective chromatin clearance in the development of cardiovascular disease and linking COVID-19 susceptibility to pre-existing conditions. Hence, the combination of aberrant chromatin release with defects in protective clearance mechanisms lead to poor survival outcomes.
An mRNA vaccine elicits STING-dependent antitumor immune responses
Authors: Zhe Chen, Chaoyang Meng, Junhua Mai, Yongbin Liu, Hangwen Li, Haifa Shen
Journal: Acta Pharmaceutica Sinica B (2022)

Lipid-formulated RNA vaccines have been widely used for disease prevention and treatment, yet their mechanism of action and individual components contributing to such actions remain to be delineated. Here, we show that a therapeutic cancer vaccine composed of a protamine/mRNA core and a lipid shell is highly potent in promoting cytotoxic CD8+ T cell responses and mediating anti-tumor immunity. Mechanistically, both the mRNA core and lipid shell are needed to fully stimulate the expression of type I interferons and inflammatory cytokines in dendritic cells. Stimulation of interferon-β expression is exclusively dependent on STING, and antitumor activity from the mRNA vaccine is significantly compromised in mice with a defective Sting gene. Thus, the mRNA vaccine elicits STING-dependent antitumor immunity.
Contents
Authors: Sandeep Ravindran, Russell Van Gelder, Steven Gedde, William Feuer, Kin Lim, Keith Barton, Saurabh Goyal, Iqbal Ahmed, James Brandt, Siamak Yousefi, Louis Pasquale, Michael Boland, Chris Johnson, Tahreem Mir, Sumarth Mehta, Karen Qiang, Ron Adelman, Lucian Priore, Jessica Chow
Journal: Ophthalmology (2022)
Author correction to ‘Protective effects of VMY-2-95 on corticosterone-induced injuries in mice and cellular models’ [Acta Pharmaceutica Sinica B 11(2021) 1903–1913]
Authors: Ziru Yu, Dewen Kong, Yu Liang, Xiaoyue Zhao, Guanhua Du
Journal: Acta Pharmaceutica Sinica B (2022)

[This corrects the article DOI: 10.1016/j.apsb.2021.03.002.].